Wondering when we can go back to school? Concerts? Movies? These Chicago ecologists are helping decide

She is working from home, and by now the routine has become fairly predictable: She wakes up and does a little yoga, she showers and pours a cup of tea, she logs into work and then she stays there, for a long, long while. Her makeshift office is in the guest bedroom of her South Loop apartment, overlooking the lake. She conducts about eight Zoom meetings, every day, and her days, these days, have been running from early morning until midnight.

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Because Sarah Cobey is working to get you back to work, school, concerts, brunch, theater, church, birthday parties, book signings and binge shopping — you remember socializing?

So, she is creating something you’ve heard about.

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She is creating predictive models. Which she then presents to the governor’s office so they can decide ultimately when you no longer have to stay home, attend school in pajamas or work in a guest bedroom. She is predicting the impact on hospitals, and even the amount of supplies those hospitals might need. She is pooling and assessing data, running it though models and saying, do this, this and this — or don’t do this, this and this — and this happens and life returns. She, along with a group of current or former lab members from University of Chicago, specifically the Department of Ecology and Evolution, are running scenarios, daily, constantly, to understand how coronavirus will spread or ebb, depending on the conditions.

They, the state, the hospitals, the schools, the Lyric Opera, the Hideout, Chicago Comics — us — everyone wants to know a lot of stuff. The state, in particular, wants to know: if social distancing is working; if we social-distance until this date, will things get better; how soon before we can reopen schools; how long before we can lift shelter-in-place orders; how many hospitals beds will Cook County need; how many ventilators; could restaurants open before stores, or could stores open before restaurants; without shelter-in-place, what happens to hospitals; if interventions stop, the death rate will do ... what?

Modeling is not the sexiest job, and often hard to grasp, but since we’re all trying ...

“In an ideal world the average person would not have to think very deeply about (scientific) modeling,” she says, “in a perfect world, for a crisis like this, that information would get parsed by someone charged with a public health response, and the state has shown some leadership there — they are synthesizing the competing models and trying to present the best information. But — you know, everyone is just scrambling right now.”

She sighs, she looks worried.

She runs a University of Chicago lab that focuses, in more normal times, on the co-evolution of pathogens and their hosts; she considers stuff like the spread of influenza across age groups, how vaccination affects transmission and how immunity impact the evolution of influenza. All of their work is being done remotely now. Her coronavirus team of 10, in their late 20s and 30s — picture Ph.Ds on laptops, in dining-room tables and bedrooms across Chicago (and California) — are handling data, not COVID-19 patients. They are building mathematical models to test hypothetical coronavirus situations. Cobey is quick to note: “We’re not the ones out there with the highest risk to health, we’re not doctors and nurses.”

At the same time, she adds, “it does get challenging, reading in newspapers about misguided ideas about pandemics, and seeing officials talking about models — like certain ones touted by this White House — and wondering how we are fitting into actual policy.”

Not to mention, said Jaline Gerardin, an assistant professor of preventive medicine at Northwestern University, deadlines for predictive models “always seem to be yesterday.”

Gerardin runs another, smaller team modeling virus transmission and providing scenarios to the state, Illinois Department of Public Health and Northwestern hospitals. There are actually a handful of groups in Illinois producing predictive models, including at Argonne National Laboratory and Nigel Goldenfeld and Sergei Maslov from the physics department at University of Illinois, Urbana-Champaign. And they are all being asked similar questions:

“Last week they wanted to know the number of ventilators we’ll need,” Gerardin said. “This week they will want to know about procuring supplies, going as far in advance as we can tell them to act. Then there’s that much hazier question of when they can lift social-distancing.”

Sylvia Ranjeva is a member of a team of ecologists and epidemiologists at the University of Chicago who are building predictive modeling that will help the state decide when to lift the shelter-in-place order. The team members are all working from their homes. (E. Jason Wambsgans / Chicago Tribune)

Cobey’s team is modeling about a month into the future, sometimes longer. And again, they’re not always certain how their work is being interpreted by bureaucracies. But the fact that a phrase like “flattening the curve,” born out of a data-based, epidemiological principle, “is so commonplace now in culture is actually pretty encouraging,” said Sylvia Ranjeva, a member of Cobey’s team. “It speaks to how people are trying to understand things, and how a lot of work that goes into fighting a virus does go on under the table.”

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Cobey is best described as an epidemiologist, mathematical ecologist, evolutionary biologist. She works with computations to understand the relationship between viral diseases and people. She grew up in Silicon Valley, and when I ask how someone gets interested in mathematical ecology, she appears stumped by the question, as if answers are obvious.

“I suppose I was just excited by the realization that pathogens, undoubtedly a source of suffering in the world, evolve incredibly fast, and that our own day-to-day evolutions affect that evolution. So this is a way to do good. And there is so much to study here. I would love to know, for instance, what is regulating the diversity of flus in the world. We don’t even understand yet why a flu starts and why a flu ends.” As she once told NPR, “I’m really interested in the question of whether we can drive the flu extinct in humans.”

Cobey is not the only mathematical ecologist, of course. Among her department colleagues at the University of Chicago, Greg Dwyer also focuses on the evolution of pathogens, though with an emphasis on insects. (He’s one of the country’s leading researchers on the boom-and-bust cycles of gypsy moths.) He said that Cobey “realized before a lot of people just how important, and biologically realistic, computational epidemiology can become. To the extent that expertise like that may go unrecognized by the public during a pandemic? Your guess is as good as mine. But I think someone like Sarah, she’s probably feeling she has been preparing a lifetime for this moment.”

Indeed, Cobey said by late January, “everyone in my field knew what would happen.” She said “spillover events” — watersheds in epidemiology when a virus spills into a population (though doesn’t necessarily transmit) — “are hard to predict but those who study them had a coronavirus at the top of their lists.” She remembers sitting in on a meeting between modeling groups and the Centers for Disease Control and Prevention and seeing the magnitude. She contacted the provost’s office at her university, sent messages to the Chicago Department of Public Health — she was alarmed at how delayed the response was. (She said that the Department of Public Health didn’t respond to her for a couple of weeks.)

Sarah Cobey of the University of Chicago's Department of Ecology and Evolution is part of a team working on modeling for the coronavirus pandemic. Here in her South Loop apartment with her dog Copper. (Provided by Sarah Cobey)

After Illinois Gov. J.B. Pritzker mentioned the modeling (from UIUC’s physics department) that helped inform his order for a state quarantine, Cobey gathered another modeling team, one with a background in infectious diseases from the Department of Ecology and Evolution.

The simplest explanation, Cobey said, is to consider the flu, and that we are asked annually to get vaccinated because strains evolve quickly, and that a large part of ecology is the study of the dynamics that move and shape interacting populations of living things, including us.

The trouble with this coronavirus, at least now, is that we still don’t know basic information about it. Dwyer said “a pandemic can play like a hideous experiment, but one you learn from.”

So, for the time being, Cobey and Co., spread throughout across the city — the South Loop, Uptown, Hyde Park — meet each morning on Zoom, then pick away at the future.

They question the assumptions built naturally into predictive modeling.

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They discuss other models, outlooks, that day’s priorities, the next day’s hopes. Earlier this week, at their regular meeting, they looked stunned and exhausted. As much data as they are receiving — often a patchwork of aggregated information from official sources such as hospitals and health departments — methods of gathering and conveying data are spotty. Frank Wen, who was a Ph.D student in Cobey’s lab and now works on data for her, said they still don’t know enough about who’s dying at home or changes made in who gets tested.

“It’s also just hard to figure out what is going on the start of an epidemic,” he said, “there are fewer data points, but gradually as (an epidemic) goes on, that picture gets clearer.”

Phil Arevalo, a postdoctoral researcher for Cobey, said the result is so many competing ideas that “I’ve heard someone say this is what climate scientists feel like all the time.”

They don’t know how long they’ll be doing this.

Maybe weeks, maybe months. They suspect that you want to know the future. They get asked for quick takeaways. Cobey, asked for the future, says it’ll be great if they find out (and they expect to find out) that sheltering in place is slowing the pace of transmission. “But as for the future, and how much life returns to normal, I’m worried, right now, it’s very little.” You can hear a wariness in her voice, and maybe the slightest of hopes for all of this to be over.